Comparisons include:
- GeneMarkS-T and -SS (strand-specific mode)
- Prodigal and -SS
- TransDecoder and -SS, -noRS (no refine-start), AGO (all good orfs)
- LongOrfs and -SS
Benchmarking methods:
- 3prime: only a 3-prime coordinate match is required for TPs.
- 5,3prime: both a 5-prime and 3-prime coordinate match are required for TPs - else if 3'-only, treated as FN.
Mouse reference sequences
Mouse reference sequences + random sequences
Mouse ref + random, TransDecoder run with varied parameter settings
Drosophila reference sequences
Drosoph + random
Drosoph + random, TD varied params
Arabidopsis reference sequences
Arabidopsis + random
Arabidopsis + random, TD varied params
S. pombe reference sequences
S. pombe + random
S. pombe + random, TD varied params